I've had it occasionally in my recent Crusade games. The last game I played I saw it on the planet of another race. I've never been able to clear it when it happens to my planet. It still existed after I saved the game, quit GalCiv3, the restarted and loaded the next day.

It's in Crusade / fully patched via steam. And it even affects one of my influence worlds. Here's the story. Influenza was taken over by the enemy. I had a serious legion crisis. So I spammed a bunch of starbases to try and make it flip. EVERY one of the starbases around it are influence. It didn't flip. The transport eventually made it over and took over. I left a legion there. And the planet is an influence based one with lots of influence items on it. That influence has been handy in voting. They also have phantom ships that show in orbit. 8) I go over to cleanse them from orbit and poof - they are not there. I have to have a corruput save file.